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Consensus

By Jackman S., Birol I., Last update 1494698999
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Consensus description

Consensus read alignments from KAligner. Ensure that the --seq option was used when running KAligner. Call a consensus at each position of each contig and write the consensus in FASTA format to OUTPUT.


Parent program: abyss

ABySS is a de novo sequencing assembler developed for short reads of large genomes. It has novel scaffolding algorithm capable of assembling very large genomes including human genomes (>3.5 billion paired-end reads). ABySS algorithm eliminates ambiguities in the scaffold graph and identifies contigs that are assembled into scaffolds.The assembly runs in three stages: assemble contigs without paired-end information, align the paired-end reads to the initial assembly, and merge contigs joined by paired-end information.